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How Gut Health Affects Your Immune System

Introduction to the Gut

Your gut is home to a massive number of microbes collectively called the gut microbiota. There are 38 trillion of these bacteria, equal to the number of cells you have in your whole body. Their total genome is called the gut microbiome and has 150 times more genes than the total human genome.

The gut health and immune system are closely related to each other; the microbiome affects human physiology in many ways, such as the nervous system, cardiovascular system, and metabolism. In this post, you will learn how the interaction between the immune system and gut microbiota affects your immune system and overall health.

Introduction to the Immune System

Your immune system is the collection of molecules and cells that save you from disease by constantly monitoring your body and fighting off external harmful substances, especially pathogens. Your immune system protects you against infectious microorganisms, while also allowing your body to accept good microbes. Thus, the gut microbiota and immune system have a mutual relationship, monitoring and supporting each other. The significance of gut health and the immune system is underscored by the fact that 80% of your body’s immune cells are present or originate in the gut.

The negotiation between the gut microbiota and the immune system begins at the time your body comes in contact with the microbes of your mother at the time of birth. As you grow, your immune system starts the formation of the microbiota, and the microbiota begins the expansion of your immune system. This mutualistic relationship and two-way communication are regulated for your whole life, and it is the key to your health.


The important substance responsible for communication between the gut microbiota and the immune system is immunoglobulin A (IgA). It is a kind of antibody made by specific B cells commonly called plasma cells. IgA can coat and bind particular microbial components, microbes, antigens, and dietary components in the intestine. This creates an extra physical barrier that avoids harmful contact with the immune system. The other kind of cells that play an important part are helper “T” cells. TH17 cells are located in the intestinal wall, which increases the permeability of the mucosal intestinal barrier, motivates the production of IgA antimicrobial proteins, thereby having a positive role in inhibiting infection and regulating homeostasis.

Role of the Intestinal Barrier

The intestinal wall is the main barrier among the gut microbiota and your body. It works as an active barrier that separates your body from gut microbes but permits required communication to take place. The intestinal fence is made of chemical and physical elements. This intestinal chemical barrier is made of pro-inflammatory cytokines, antimicrobial substances, and antibodies produced by immune and epithelial cells. The other physical barrier is made of epithelial cells that are present in the lining of the gut, that produce mucus, and the particles on their surface.

Bacteria tells your immune system how to work

Gut health and the immune system are regulated by the many types and number of bacteria in your body. The immune system is the key link between your gut bacteria and their effect on your disease and health. We now know that this process begins even before you are born. It was formerly believed that the prenatal atmosphere in the mother’s womb was free from bacteria, but fortunately, due to advanced diagnostic methods, we now know that bacteria are found in the placenta. You have a built-in innate immune system and are first sheltered by antibodies from your mother. From there, the immune cells need to be polished more to learn how to secure the body from harmful micro-organisms when the maternal antibodies are not present. This training is necessary for your lifetime health.

Plant fibers have an important role in gut health and the immune system

A plant-based diet provides insoluble dietary fiber and carbohydrates like pectin and oat bran, which are fermented by specific microbial species into short-chain fatty acids (SCFAs) like butyrate and acetate in the intestine. They also enhance the action of regulatory T cells. These cells avoid inflammatory responses against beneficial intestinal microorganisms by down-regulation of the irregular activity of helper T and immune cells. Treg cells play a significant role in the production of the dietary compound, self-antigen, and in preserving immune acceptance of the gut microbiota.

SCFAs also maintain the integrity of the intestinal mucosal epithelial barrier, enhance gut homeostasis, more production of IgA by reducing pro-inflammatory responses, and promoting intestinal secretions.

Diverse gut microflora is the healthiest

It is not so simple to permanently alter an already developed gut microflora, for bad or good. But if you eat a balanced diet, rich in pro and prebiotics, this will help to diversify the microflora. Then the changes in flora should revert to normal condition within a short duration of time, just like as you come back home after a holiday and resume your routine diet.

 Harmful gut bacteria can cause disease

Several bacteria are healthy, but some are responsible for the development of the disease. It is, therefore common sense that gut microbiota plays a vital role in diseases directly associated with the gut, such as inflammatory bowel diseases. Studies show that treatments are present to correct disturbed bacterial species and help in the recovery of harmless bacteria through fecal transplantation in some patients with colitis. Research studies have also shown that specific bacterial species are involved in the onset of obesity and type 1 diabetes. The researchers were able to cause mice to become obese by introducing harmful bacteria into their gut.

The Bottom Line on your Gut

A beneficial and healthy relationship between your gut microbiota and your immune system is essential for the regulation of your body’s health and homeostasis. Disturbance in the gut microbiota may lead to the onset of autoimmune responses and chronic inflammatory diseases. That is why it is crucial to take the best care of our gut with pro and prebiotics. And this will starts with what you intake.


1-A.K. Abbas, A.H.H. Lichtman, S. Pillai, Cellular and Molecular Immunology E-Book, Elsevier Health Sciences, 2017.
2- A. Trompette, E.S. Gollwitzer, C. Pattaroni, I.C. Lopez-Mejia, E. Riva, J. Pernot, N. Ubags, L. Fajas, L.P. Nicod, B.J. Marsland, Immunity 48 (2018) 992–1005.e8
3- how the gut microbiota influences our immune system 2019, July 8.
4- why gut bacteria are essential for a healthy immune system 2018, march 29

Author: Dr. Zohaib

Dr. Zohaib possesses a Mphil and PhD in Physiology. He has a special interest in Oncology as a research topic.

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